A Computer Model of Field-Directed Morphogenesis Part I - Julia Sets

A Computer Model of Field-directed Morphogenesis Part I - Julia Sets Michael Levin Genetics Dept. Harvard Medical School (617) 432-7758 Inet: [email protected] Running title: "Julia set model of field-driven development" Summary One paradigm used in understanding the control of morphogenetic events is the concept of positional information, where sub-organismic components (such as cells) act in response to positional cues. It is important to determine what kinds of spatio-temporal patterns may be ob- tained by such a method, and what the characteristics of such a morphogenetic process might be. This paper presents a computer model of morphogenesis based on gene activity driven by interpreting a positional information field. In this model, the interactions of mutually-regulating developmental genes are viewed as a £¡ map from ¢¡ to , and are modeled by the complex number algebra. Functions in complex variables are used to simulate genetic interactions resulting in position-dependent differentiation. This is shown to be equivalent to computing modified Julia sets, and is seen to be sufficient to produce a very rich set of morphologies which are similar in appearance and several important characteristics to those of real organisms. The properties of this model can be used to study the potential role of fields and positional information as guiding factors in morphogenesis, as the model facilitates the study of static images, time-series (movies), and experimental alterations of the developmental process. It is thus shown that gene interactions can be modeled as a multi-dimensional algebra, and that only two interacting genes are sufficient for 1) complex pattern formation, 2) chaotic differentiation behavior, and for 3) production of sharp edges from a continuous positional information field. This model is meant to elucidate the properties of the process of positional information- guided bio-morphogenesis, not to serve as a simulation of any particular organism’s development. Good quantitative data is not currently available on the interplay of gene products in morphogenesis. Thus, no attempt is made to link the images produced with actual pictures of any particular real organism. A brief introduction to top-down models and positional information is followed by the formal definition of the model. Then, the implications of the resulting morphologies to biological development are discussed, in terms of static shapes, parametrization studies, time series (movies made from individual frames), and behavior of the model in light of experimental perturbations. All figures (in grayscale1), formulas, and parameter values needed to re-create the figures and movies are included. 1 Color slides and videotapes are available from the author. Introduction The Biology of Artificial Life Computer models can serve as biological theories (as in Partridge and Lopez, 1984, Gar- finkel, 1984). The rapidly growing field of Artificial Life uses computer models to emphasize the common processes and characteristics of living things, rather than their physico-chemical implementation. The accent is on the role of bioinformation, cybernetic control processes, complexity and systems theory, rather than the study of specific instances of physicochemical processes (Apter, 1966, Narendra and Thompson, 1986, Langton, 1990, Langton, 1991). "Computer simulations provide the experimental biologist with a much needed means for doing experiments on theories. We usually think of experiments as something performed on cells, to determine whether the cells’ responses will match predictions made by a theory. However, when dealing with complex phenomena and with correspondingly complex theories, what a given hypothesis predicts can be less than obvious. It can be even more difficult to perceive which components in the hypothesis give rise to a particular prediction, much less to know what alterna- tive classes of hypothesis would have predicted the same results. Lastly, anyone with sufficient insight to predict the consequences of a given theory may need ob- jective methods for proving it to others. Computer simulations can help solve all these problems." (Harris, 1990) This approach is at the intersection of biology, mathematics, physics, and computer science, and has mainly involved computer models of behavior or evolution. Some attempts to model various developmental phenomena (such as cell proliferation, cleavage, cell migration, specific pattern formation, etc.) by creating computer simulations of the behavior of the underlying components have been made (Ransom, 1981, and Meinhardt, 1982, are good summaries of such efforts). Interesting special cases are found in Düchting and Vogelsaenger, 1984 and 1985, and Thom, 1983. Good examples of the common "bottom-up" model (where the desired phenomenon emerges from a simulation of empirically-derived behaviors of lower-level components) can be found in Goel and Rogers, 1978, and Rogers and Goel, 1978. In the "top-down" model (sometimes termed "informal", Conrad, 1981), the researcher cre- ates a computer simulation which behaves like the system modeled (in some interesting way), without too much regard for the empirical validity of specific lower-level components; the model’s empirical fitness is tested at a higher level. This approach can be used to study characteristics of processes or general schemes. For example, one may create a well-fitting model of some animal’s social behavior based on general principles of cooperation, game theory, and information theory, without any regard as to whether the components of the equations have any physical counterparts in the animal’s brain (for example, Krebs et al., 1978, Axelrod and Ham- ilton, 1981). These kinds of models usually precede bottom-up models, and are much more common in ethology, evolutionary theory, and the cognitive sciences than in developmental biology. Excellent examples of top-down models are given in Raup and Michelson, 1965, Rozen- berg and Salomaa, 1986, and Slack, 1991. L-systems (Lindenmeyer, 1989, Prusinkiewicz and Lindenmeyer, 1990) are among the best examples of top-down models because they possess the appropriate higher-order behavior even though there is no known physical mechanism in plants -1- which explicitly implements the symbol manipulation rules used in an L-system. Kauffman’s work (1969, 1974, 1990) with dynamics of abstract logic elements networks is another good example, since these studies capture higher-order rules governing gene interactions without using characteristics of real genes. Whereas the bottom-up model tries to be as realistic and focused as possible, providing empirically-accurate data of some narrow and specific aspect of development (for example, Ransom et al., 1984, and Meinhardt, 1984), the top-down model attempts to derive the overall pattern of control, information flow, and higher-order characteristics at the cost of losing some lower-level realism. Bottom-up models are able to provide more concrete information about some narrowly-defined process; the benefit of the top-down model is that it allows insight into the higher-order properties of processes, and can be used when sufficient data and/or theory for a bottom-up model is not available. These models are useful in the study of developmental morphogenesis because embryonic development is very likely to involve general mechanisms of in- creasing complexity; at the same time, much low-level data (such as quantitative mechanisms of gene interactions) is currently unavailable. This paper presents a positional field-driven model of development which is intermediate between the bottom-up and top-down types. Positional information and field concepts in biology The basic problem of pattern formation can be viewed from one (or a combination) of two general perspectives. The developing organism’s resulting morphology can be seen as a product of subunits following a sort of master plan - a blueprint (at some level of detail) of the whole organism. Or, it may be an emergent phenomenon, where the overall pattern emerges as the re- sult of purely local interactions between subunits governed by rules which say nothing about the overall pattern (best exemplified by cellular automata systems, as in Gutowitz, 1991). An intermediate paradigm involves positional information (Wolpert, 1969, 1971, 1989). That is, each unit (usually thought of as a cell, but this could apply equally well to tissues, cell sheets, or sub-cellular components) is able to determine its position within the organism, and act (differentiate, migrate, proliferate, etc.) based upon that positional information. The positional information is usually thought of as coordinates in a field, which then can be a mechanism for long-range control and information transfer (see Cooke, 1975 for a review of field theories in biology). The paradigm is thus a combination of the two approaches in that it in- cludes both purely local decision-making (with an emphasis on the distinction between the field itself, and various components’ responses to it), as well as a global entity (the positional information field itself). In this view, the overall morphology emerges from units following rules which specify actions based on the unit’s position; the process of morphogenesis can be "char- acterized as a series of solutions of the morphogenetic field whose superposition gives way to complex stable patterns." (Goodwin, 1988). The role of positional information in early development is reviewed

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